[2026-05-28T00:13:45] Launching Arriba 2.4.0
[2026-05-28T00:13:45] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:13:54] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:13:58] Reading chimeric alignments from 'tih_rna_sample_00434_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=3257489)
[2026-05-28T00:16:10] Marking multi-mapping alignments (marked=2007478)
[2026-05-28T00:16:11] Detecting strandedness (reverse)
[2026-05-28T00:16:11] Assigning strands to alignments 
[2026-05-28T00:16:11] Annotating alignments 
[2026-05-28T00:16:23] Filtering duplicates (remaining=2211096)
[2026-05-28T00:16:25] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=2120357)
[2026-05-28T00:16:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2120357)
[2026-05-28T00:16:26] Filtering viral contigs with expression lower than the top 5 (remaining=2120357)
[2026-05-28T00:16:27] Filtering viral contigs with less than 5% coverage (remaining=2120357)
[2026-05-28T00:16:28] Estimating fragment length (mate gap mean=-87.4038, mate gap stddev=28.0679, read length mean=131.244)
[2026-05-28T00:16:28] Filtering read-through fragments with a distance <=10000bp (remaining=1940148)
[2026-05-28T00:16:29] Filtering inconsistently clipped mates (remaining=1905398)
[2026-05-28T00:16:29] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1867786)
[2026-05-28T00:16:31] Filtering fragments with small insert size (remaining=1867504)
[2026-05-28T00:16:31] Filtering alignments with long gaps (remaining=1867504)
[2026-05-28T00:16:32] Filtering fragments with both mates in the same gene (remaining=1867147)
[2026-05-28T00:16:33] Filtering fusions arising from hairpin structures (remaining=1752166)
[2026-05-28T00:16:34] Filtering reads with a mismatch p-value <=0.01 (remaining=842173)
[2026-05-28T00:16:38] Filtering reads with low entropy (k-mer content >=60%) (remaining=434162)
[2026-05-28T00:16:42] Finding fusions and counting supporting reads (total=352463)
[2026-05-28T00:16:48] Merging adjacent fusion breakpoints (remaining=350070)
[2026-05-28T00:16:48] Filtering multi-mapping fusions by alignment score and read support (remaining=228736)
[2026-05-28T00:16:59] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:17:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=227722)
[2026-05-28T00:17:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=111294)
[2026-05-28T00:17:02] Filtering fusions with <2 supporting reads (remaining=16317)
[2026-05-28T00:17:03] Filtering fusions with an e-value >=0.3 (remaining=5110)
[2026-05-28T00:17:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5158)
[2026-05-28T00:17:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5136)
[2026-05-28T00:17:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5136)
[2026-05-28T00:17:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4104)
[2026-05-28T00:17:07] Searching for fusions with spliced split reads (remaining=4138)
[2026-05-28T00:17:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=2839)
[2026-05-28T00:17:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2804)
[2026-05-28T00:17:09] Searching for fusions with >=4 spliced events (remaining=3086)
[2026-05-28T00:17:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=856)
[2026-05-28T00:17:21] Filtering fusions with anchors <=23nt (remaining=708)
[2026-05-28T00:17:22] Filtering end-to-end fusions with low support (remaining=688)
[2026-05-28T00:17:22] Filtering fusions with no coverage around the breakpoints (remaining=671)
[2026-05-28T00:17:22] Indexing gene sequences 
[2026-05-28T00:17:25] Filtering genes with >=30% identity (remaining=236)
[2026-05-28T00:17:26] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=135)
[2026-05-28T00:17:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=135)
[2026-05-28T00:17:29] Searching for additional isoforms (remaining=149)
[2026-05-28T00:17:30] Assigning confidence scores to events 
[2026-05-28T00:17:31] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:17:31] Writing fusions to file 'tih_rna_sample_00434_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-05-28T00:17:32] Writing discarded fusions to file 'tih_rna_sample_00434_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T00:17:44] Freeing resources
[2026-05-28T00:17:50] Done (elapsed time=00:04:05, CPU time=00:04:04, peak memory=7.63gb)